PB1911: CYTOGENOMIC INTEGRATIVE ANALYSIS OF CLL/SLL PATIENTS AT DISEASE PROGRESSION.
Authors: Rocío García-Serra, Marisol Uribe, Olga Mompel, Cristina Játiva, Asunción Cámara, Margarita Monzó, Maria José Lis, Carmen Amorós, Maria Teresa Orero, Mariano Linares, Mariam Ibáñez Comany, Rosa Collado Nieto
Journal: HemaSphere (2023)

Topic: 5. Chronic lymphocytic leukemia and related disorders - Biology & Translational Research Background: CLL is a very heterogeneous disease with a highly variable clinical course ranged from asymptomatic cases remaining stable for years to a rapid disease progression and need of treatment. The study of chromosomal alterations in patients with CLL remains essential, due to their impact on prognosis and clinical management. Currently, the determination of these alterations is mainly performed by standard of care techniques: chromosome banding analysis (CBA), genomic microarrays and fluorescence in situ hybridization (FISH). However, due to the technical limitations of these methodologies, some alterations can be masked. Optical genome mapping (OGM) allows the detection of genome-wide chromosomal abnormalities, rearrangements and structural alterations in a single experiment, with high resolution and sensitivity. Aims: This study aims to describe the impact of OGM on improving the genetic characterization of CLL/SLL patients at disease progression. Methods: A total of 12 patients diagnosed with CLL (n=11) and small lymphocytic lymphoma (SLL) (n=1) with available CBA, FISH and next generation sequencing (NGS) (Sophia Genetics® CCLL-V3 gene panel) results were studied at progression. Ultra-high molecular weight (UHMW) DNA was extracted from peripheral blood and analyzed by OGM (Bionano Genomics). Genomic analysis was performed using the Bionano Solve program and the Bionano Access viewer v1.7 by the Rare Variant Pipeline (RVP). Whenever possible, the detected variants were further confirmed by FISH. Results: OGM identified chromosomal aberrations in all patients, the median number of abnormalities/case was 6,5 (range: 2-47) (Figure 1). The most common alterations were intra e interchromosomal translocations (n=69), followed by 34 losses and 19 gains. Two patients (#1 and #2) displayed chromothripsis affecting chromosomes 5 and 9, and 10, respectively. Overall, 122 cytogenomic alterations were detected by the combination of OGM, CBA and FISH. OGM was 95.9% concordant with CBA and FISH, and showed 76 additional alterations overlooked by classical techniques. Discordances (n=5) were found in the p-arm of acrocentric chromosomes (chromosomes 13 and 21), dicentric chromosomes and subclonal aberrations seen in a small proportion of metaphases. In addition, alterations already detected by CBA were redefined and some marker chromosomes were identified. OGM also revealed 20 unexpected putative fusion genes, of which the following might be relevant due to the clinical impact of the involved genes: BCL2::IGLL5, DLEU2::RNASEH2B and BCL11::IGHG1. Furthermore, 11/12 patients showed somatic variants by NGS. We detected 15 mutations, being 47% of them pathogenic, 33% likely pathogenic and 20% VUS (Figure 1). The most frequent mutated gene was TP53 (17p13) (n=5), followed by NOTCH1 (9q34) (n=2) and SF3B1 (2q33) (n=2) and 75% presented unmutated IGHV. Finally, genomic complexity observed in chromotriptic cases was accompanied by high-risk biomarkers as TP53 mutations and unmutated IGHV. Summary/Conclusion: 1. The present study has shown that OGM is a very useful tool to deepen our understanding of cytogenomic complexity in patients with CLL/SLL during the progression stage. 2. The application of OGM allows us to refine the alterations previously displayed by conventional techniques (chromosome banding analysis and FISH), as well as to detect new biomarkers of potential clinical interest. 3. OGM results together with sequencing data could contribute to improve risk stratification, leading to personalized treatment choices. Aknowledgements: G-S R was supported by a predoctoral contract (ACIF/2021/169) from the Consellería de Innovación, Universidades, Ciencia y Sociedad digital (Generalitat Valenciana).Keywords: Mutation analysis, B-CLL, Molecular cytogenetics